Prevalence of Co-infection during SARS-CoV-2 Pandemic and Association with Respiratory Infections

Background:The diagnostics infrastructure experienced a bottleneck during the COVID-19 pandemic.Most qPCR-based diagnostic settings have primarily aimed at detecting SARS-CoV-2 to isolate the cases and contain the spread of infection.As the number of SARS-CoV-2 cases, which shares a similar transmission mode with other common respiratory viruses surged at alarming rate.The worldwide trend showed a sharp decline in the cases of other respiratory viruses, including influenza A virus.The study aims to evaluate the circulation of different respiratory viruses in the positive and negative samples for SARS-CoV-2, collected from symptomatic individuals.Methods: The RT-qPCR-based detection assays for SARS-CoV-2 viral RNA were used in all the clinical samples collected from the symptomatic individuals.In addition, a qPCR-based diagnostic kit evaluated the prevalence of other respiratory viruses in randomly selected positive and negative samples.Results: Out of 4,123 nasopharyngeal samples tested, 622 were found to be positive for SARS-CoV-2 viral RNA, indicating an overall positivity rate of 15.0%.Among these positive cases, four samples exhibited co-infection with other respiratory viruses.Notably, 34% of the samples that did not contain SARS-CoV-2 were instead found to be infected with other respiratory viruses.Conclusion: Our findings reveal that respiratory viruses, apart from SARS-CoV-2, continue to be widespread in the community.Moreover, the SARS-CoV-2 virus infection is not mutually exclusive, indicative of co-infection with other respiratory viruses.The prevalence of the influenza A virus is also notably high.Therefore, our data suggest that multiplexed-qPCR detection assays could also be employed to screen patients presenting flu-like symptoms for other respiratory viruses.